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[190673_s_at]

Description F47A4.1 /REP_DB=WormBase Gene ID /WP=CE16057 /TR=Q20105 /GB=CAA90065.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=ligand gated ion channel
Cluster 6grp_total > 15      4grp_total > 31      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 209
1 2 3 4 range
A 162.4
(3)
P 		60.8
(-1.2)
A 		18.7
(-3)
A 		143.1
(2.2)
A 		144
B 227.3
(3)
P 		24.5
(-2.8)
A 		18.8
(-3)
A 		59.7
(-1.8)
A 		209
C 179.7
(3)
P 		44.7
(-3)
A 		77.8
(-1.5)
A 		125.1
(0.6)
A 		135
avr 189.8
(3) 		43.3
(-2.8) 		38.4
(-3) 		109.3
(-0.2) 		151

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 132
1 2 3 4 5 6 range
A 21.4
(-2.1)
A 		89.1
(3)
A 		9.3
(-3)
A 		13.1
(-2.7)
A 		65.2
(1.2)
A 		16.2
(-2.5)
A 		80
B 51.6
(1.3)
A 		61
(2.4)
A 		66.4
(3)
A 		14.8
(-3)
A 		59.4
(2.2)
A 		21.7
(-2.2)
A 		52
C 141
(3)
P 		67.2
(-0.4)
A 		52.1
(-1.1)
A 		10.3
(-3)
A 		10.8
(-3)
A 		10.1
(-3)
A 		131
avr 71.3
(2.9) 		72.4
(3) 		42.6
(0) 		12.7
(-3) 		45.1
(0.3) 		16
(-2.7) 		60
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 68
1 2 3 4 range
A 59.1
(3)
P 		13.2
(-2.1)
A 		4.9
(-3)
A 		21
(-1.2)
A 		54
B 72.5
(3)
P 		6.1
(-2.8)
A 		4.3
(-3)
A 		12.7
(-2.3)
A 		68
C 59.5
(3)
P 		12.9
(-3)
A 		27.1
(-1.2)
A 		21.1
(-1.9)
A 		47
avr 63.7
(3) 		10.7
(-3) 		12.1
(-2.8) 		18.3
(-2.1) 		53

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 50
1 2 3 4 5 6 range
A 4
(-2.6)
A 		31.7
(3)
A 		2
(-3)
A 		3.3
(-2.7)
A 		19.7
(0.6)
A 		3.9
(-2.6)
A 		30
B 18
(1.2)
A 		20.3
(1.9)
A 		16.1
(0.6)
A 		3.9
(-3)
A 		24.1
(3)
A 		8.1
(-1.8)
A 		20
C 52.3
(3)
P 		20.5
(-0.8)
A 		13.3
(-1.7)
A 		2.1
(-3)
A 		3.5
(-2.8)
A 		3.4
(-2.8)
A 		50
avr 24.8
(3) 		24.2
(2.8) 		10.5
(-1) 		3.1
(-3) 		15.8
(0.5) 		5.1
(-2.4) 		22
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190673_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17093
Sequence Type Exemplar sequence
Representative Public ID F47A4.1 NCBI
Target Description F47A4.1 /REP_DB=WormBase Gene ID /WP=CE16057 /TR=Q20105 /GB=CAA90065.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=ligand gated ion channel
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_171756, NM_171757
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
F47A4.1a ENSEMBL cdna:known chromosome:CEL140:X:9801022:9807447:-1 gene:F47A4.1 None
F47A4.1b ENSEMBL cdna:known chromosome:CEL140:X:9801405:9807409:-1 gene:F47A4.1 None
NM_171757 NCBI Caenorhabditis elegans F47A4.1a (F47A4.1) mRNA, complete cds. None
NM_171756 NCBI Caenorhabditis elegans F47A4.1b (F47A4.1) mRNA, complete cds. None
GENEFINDER00000039709 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:9803824:9807959:-1 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000039705 4/11 Cross Hyb Matching Probes None
GENEFINDER00000015724 2/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:9801404-9807497(-) 100.0 100.0
Public Domain and Genome References
Ensembl F47A4.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAD44128 Hypothetical protein F47A4.1b [Caenorhabditis elegans] emb|CAD44131.1| Hypothetical protein F47A4.1b [Caenorhabditis elegans] ref|NP_741878.1| F47A4.1b [Caenorhabditis elegans] 0.0
blast CAA90065 Hypothetical protein F47A4.1a [Caenorhabditis elegans] emb|CAA87339.2| Hypothetical protein F47A4.1a [Caenorhabditis elegans] ref|NP_741879.1| F47A4.1a [Caenorhabditis elegans] 0.0
blast CAE58713 Hypothetical protein CBG01898 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.0E-11
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.0E-70
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.0E-11
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.0E-70
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.8E-36
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.9E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_741879.1 4 248-270,275-297,312-334,383-400
NP_741878.1 5 15-32,266-288,298-317,330-352,402-419
F47A4.1a 4 248-270,275-297,312-334,383-400
F47A4.1b 5 15-32,266-288,298-317,330-352,402-419
GENEFINDER00000039709 1 422-444
Sequence
Target Sequence 
>C. ELEGANS:190673_S_AT
tctcttccgccgaaggtctggatggtatctcttgcaaggttacattccaacctatatgac
agtgttcatttcttggattccattttacttgggcccaaaagcaatacccgctcggactat
gataggtgtcaatgccctactggcgcttaccttccagtttggtaatataatccgaaacct
accacgagtgtcgtatatcaaagccatcgacgtctggatgttgaggtttgtttctgtttc
cacctcttctcttcttgtcttacctctacaattattcataacctccgcacccaaaaacct
ccacattttcttttctttcagtggcat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCTCTTCCGCCGAAGGTCTGGATGG 656 611 915 Antisense
GACAGTGTTCATTTCTTGGATTCCA 279 369 972 Antisense
TGGATTCCATTTTACTTGGGCCCAA 402 551 988 Antisense
AAAGCAATACCCGCTCGGACTATGA 38 123 1012 Antisense
GATAGGTGTCAATGCCCTACTGGCG 100 423 1035 Antisense
GGCGCTTACCTTCCAGTTTGGTAAT 142 543 1056 Antisense
ATCCGAAACCTACCACGAGTGTCGT 369 37 1084 Antisense
GAGGTTTGTTTCTGTTTCCACCTCT 76 403 1137 Antisense
TCTTCTTGTCTTACCTCTACAATTA 81 617 1164 Antisense
TACAATTATTCATAACCTCCGCACC 94 643 1181 Antisense
ACATTTTCTTTTCTTTCAGTGGCAT 368 103 1217 Antisense
Sequence Source Affymetrix Proprietary Database